With new tools that can grab individual strands of DNA
and stretch them like rubber bands, Rice University scientists are working to
unravel a mystery of modern genomics. Their latest findings, which appear in
Physical Review Letters, offer new clues about the physical makeup of odd
segments of DNA that have just one DNA base, adenine, repeated dozens of
times in a row.

These mysterious “poly(dA) repeats” are
sprinkled throughout the human genome. Scientists have also found them in the
genomes of animals, plants and other species over the past decade. But
researchers do not know why they are there, what function they perform or why
they occur only with the DNA base adenine and not the other three DNA bases — cytosine, guanine and thymine.

CHING-HWA KIANG

“Previous investigations of poly(dA) have suggested
that adenine bases stack in a very uniform way,” said Ching-Hwa Kiang, a co-author
of the new study and assistant professor of physics and astronomy at Rice.
“Our investigation focused on what happens when single strands of poly(dA)
were stretched and these stacks were pulled apart.”

Kiang’s research group specializes in studying the
physical and mechanical properties of proteins and nucleic acids, and their
primary tool is one of the mainstays of nanotechnology research — the atomic
force microscope, or AFM. The
business end of an AFM is like a tiny phonograph needle. The tip of the needle
is no more than a few atoms wide, and the needle is at the end of an arm that
bobs up and down over the surface of what is being measured. While
nanotechnologists use the device to measure the thickness of samples, Kiang’s
group uses it in a different way.

To begin her experiments, Kiang first places a thin
coating of the proteins she wishes to study on a flat surface. This is placed
under the AFM arm so the bobbing AFM needle can dip down and grab the ends of
one of the proteins. As the arm retracts, it unravels the protein.

All proteins fold into a characteristic shape. Like tiny
springs, they remain in this compact “lowest energy” state unless
they are pried apart.

Rice physicist Ching-Hwa Kiang has pioneered the use of the atomic force microscope to measure the forces needed to stretch individual strands of DNA.

The new study on poly(dA) was conducted by Kiang, Rice
graduate student Wuen-shiu Chen and colleagues at Rice and National Chung Hsing
University (NCHU) in Taiwan. The team discovered that poly(dA) behaves
differently depending upon the speed with which it is stretched. When the AFM
bobbed rapidly, the poly(dA) segments behaved like any other segment of
single-stranded DNA. But when the AFM motion was slowed, the team found that
the amount of force required to stretch the poly(dA) changed. At two particular
locations, the strand lengthened for a short distance without any additional
force at all.

“Typically, single strands of DNA behave like a
rubber band: The resistance increases as they stretch, meaning you have to pull
harder and harder to continue stretching them,” Kiang said. “With
poly(dA), we found these two points where that doesn’t apply. It’s as if you
have to pull harder and harder, and then for a brief time, the band stretches
with no additional force whatsoever.”

Kiang said the exact causes and implications of the
phenomenon are unclear. But scientists know that double-stranded DNA must be
pried apart at discrete locations so that the cell’s machinery can read the
genetic code and convert it into proteins. There has been some speculation that
the adenine repeats play a role in ordering genomic information; Kiang said the
new findings raise even more questions about the role the repeats might play in
gene regulation and genome packaging and how they might be potential targets
for cancer drugs.

The research was supported by the National Science
Foundation, the Welch Foundation and the Rice Institute of Biosciences and
Bioengineering’s Hamill
Innovation Fund. Study co-authors include Rice undergraduate students
Zephan Chen and Ashton Gooding, exchange graduate student Wei-Hung Chen from
NCHU and NCHU Professor of Chemistry Kuan-Jiuh Lin.

About Jade Boyd

Jade Boyd is science editor and associate director of news and media relations in Rice University's Office of Public Affairs.